thesis-chapter

Context

Target: $ARGUMENTS

Chapters present:

!ls chapters 2>/dev/null || ls *.tex *.md 2>/dev/null | head -20 || echo "(no chapters directory)"

Research question record (head):

!head -40 research/QUESTION.md 2>/dev/null || echo "(no research/QUESTION.md; run research-question first)"

Notes available:

!ls research/notes 2>/dev/null | wc -l | xargs -I{} echo "{} notes in research/notes/"

Bibliography:

!ls *.bib references/*.bib 2>/dev/null | head -3 || echo "(no .bib found)"

Task

Produce or revise the chapter named in the arguments. A chapter is written once, in full, from an agreed outline; it is not written in fragments across sessions, because the argument has to hold across sections.

Step 1: Establish the inputs

• Resolve the target to a file (chapters/04-results.tex, chapters/04-results.md, or a new file following the existing naming). With --revise, read the current chapter in full first.
• Read research/QUESTION.md; identify which research questions this chapter serves.
• Read the outline for the chapter (a comment block at the top of the file, research/OUTLINE.md, or the proposal's chapter plan). If there is no outline, write one as a list of claims, one per intended paragraph, show it, and stop for agreement before drafting.
• Read every note in research/notes/ marked relevant to this chapter, and any results files or tables it must present.

Step 2: Draft or revise

Apply academic-writing for the section types in this chapter. Constraints:

• Every paragraph starts with its claim.
• Every citation is a key that exists in the .bib; the citation-guard hook reports misses as you write. Never add a key that is not in the file; leave [[CITE: what is needed]] for the student.
• Every number comes from a results file or a note, with its source in a comment (% from results/latency.csv row 12 or <!-- ... -->).
• Figures and tables are referenced by label before they appear; missing ones are placeholders [[FIG: what it should show]] so research-figures can produce them.
• Match the document's format: LaTeX (\section, \cite, \cref) or Pandoc Markdown (#, [@key], @fig:x).
• With --length, aim within 10% of the target; otherwise use the chapter plan's target or the department norm.
• With --revise, keep the student's sentences where they work; change structure and wording only where the section rules require it, and list what changed.